[English] 日本語
Yorodumi
- PDB-3opq: Phosphoribosylaminoimidazole carboxylase with fructose-6-phosphat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3opq
TitlePhosphoribosylaminoimidazole carboxylase with fructose-6-phosphate bound to the central channel of the octameric protein structure.
ComponentsPhosphoribosylaminoimidazole carboxylase,catalytic subunit
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Phosphoribosylaminoimidazole carboxylase / Catalytic subunit Francisella tularensis subsp. tularensis SCHU S4 / purE
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process / lyase activity
Similarity search - Function
Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FRUCTOSE -6-PHOSPHATE / FORMIC ACID / PHOSPHATE ION / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Phosphoribosylaminoimidazole carboxylase with fructose-6-phosphate bound to the central channel of the octameric protein structure.
Authors: Filippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
B: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
C: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
D: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
E: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
F: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
G: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
H: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,67438
Polymers140,3378
Non-polymers2,33730
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39070 Å2
ΔGint-330 kcal/mol
Surface area36950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.590, 96.670, 128.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Phosphoribosylaminoimidazole carboxylase,catalytic subunit


Mass: 17542.129 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Gene: FTT_0896, purE / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: Q5NGE9, phosphoribosylaminoimidazole carboxylase

-
Non-polymers , 5 types, 510 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.25 %
Crystal growTemperature: 295 K / pH: 8.5
Details: 0.2 M NH4 dihydrogen PO4, 0.1 M Tris, 2% Tacsimate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872
DetectorType: MAR CCD / Detector: CCD / Date: Aug 13, 2010 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 142585 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 10.81
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 2.47 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
CCP4model building
MrBUMPphasing
PHENIXmodel building
REFMAC5.5.0109refinement
XSCALEdata scaling
CCP4phasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.282 / SU ML: 0.128 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3744 5 %RANDOM
Rwork0.188 ---
obs0.191 70552 29.3 %-
all-70552 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--2.53 Å20 Å2
3----1.65 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9414 0 136 480 10030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229718
X-RAY DIFFRACTIONr_bond_other_d0.0010.026381
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.98213156
X-RAY DIFFRACTIONr_angle_other_deg0.95315760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68251284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19425.074339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.669151636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5651539
X-RAY DIFFRACTIONr_chiral_restr0.0810.21549
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021730
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6971.56416
X-RAY DIFFRACTIONr_mcbond_other0.1961.52630
X-RAY DIFFRACTIONr_mcangle_it1.277210231
X-RAY DIFFRACTIONr_scbond_it2.93333302
X-RAY DIFFRACTIONr_scangle_it3.8384.52925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 259 -
Rwork0.221 5203 -
obs--99.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.794-0.24750.17290.4648-0.16653.15670.0388-0.02550.22840.0472-0.04340.063-0.2659-0.27040.00460.06770.00620.0380.0718-0.01810.143219.957267.5173101.9062
20.45770.16610.23860.68480.41262.47840.02410.00280.1368-0.0770.0391-0.0456-0.36360.3208-0.06310.1016-0.0610.03850.1197-0.02520.116368.097467.981892.4687
33.02660.1506-0.27330.7575-0.30210.89080.11320.25890.3342-0.053-0.01540.0492-0.1853-0.0492-0.09780.12760.03590.02560.04820.02080.066539.106567.354872.7318
43.03990.4402-0.06070.4290.33420.72180.08060.222-0.36390.0090.0159-0.09730.13820.0612-0.09650.11010.0361-0.01820.057-0.03170.082446.045649.267172.5646
50.9391-0.4764-0.40370.68220.34342.5422-0.0237-0.1201-0.16990.05770.0436-0.06850.19990.2611-0.01990.0628-0.0026-0.00860.10370.00390.132168.812849.924599.4267
62.514-0.02990.23051.01540.50090.86580.0447-0.20610.26580.0858-0.0325-0.0172-0.15260.0472-0.01230.1409-0.0220.01020.0757-0.01090.04748.887967.6149121.1994
72.1904-0.26670.26640.4634-0.21830.74270.0839-0.1946-0.25730.0507-0.04990.02860.22480.0142-0.0340.1588-0.0327-0.00450.06010.02540.053541.422249.8432122.0262
80.84930.4748-0.02150.8008-0.20242.670.0450.0282-0.14870.0049-0.02130.07150.302-0.2286-0.02370.0855-0.02120.01170.0522-0.01290.113419.528749.446494.9914
99.8128-9.097410.788611.9726-9.322211.99250.04750.2735-0.3753-0.0370.23910.3825-0.08980.3682-0.28660.02540.00110.03190.1935-0.0790.115844.260358.545396.7914
100.33180.5020.32831.4703-0.14871.66320.1240.0435-0.0563-0.0782-0.0526-0.0963-0.0184-0.0548-0.07140.37590.06030.01760.3720.01330.36142.381159.524795.5371
110000000000000000.3031-0.02040.0240.0843-0.03160.147829.187164.866112.3735
120.0051-0.0148-0.01030.05670.04090.03090.02810.01760.0189-0.0384-0.0328-0.0239-0.0145-0.03210.00470.56960.0110.01120.12380.04710.492549.777158.844596.6403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 161
2X-RAY DIFFRACTION2B1 - 162
3X-RAY DIFFRACTION3C2 - 162
4X-RAY DIFFRACTION4D2 - 163
5X-RAY DIFFRACTION5E2 - 161
6X-RAY DIFFRACTION6F2 - 163
7X-RAY DIFFRACTION7G1 - 160
8X-RAY DIFFRACTION8H2 - 162
9X-RAY DIFFRACTION9C - G1 - 167
10X-RAY DIFFRACTION10B - G1 - 164
11X-RAY DIFFRACTION11A1 - 167
12X-RAY DIFFRACTION12E - B1 - 168

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more